VMD-L Mailing List

From: Giovanni Bellesia (gbellesia_at_chem.ucsb.edu)
Date: Wed Mar 05 2008 - 11:45:31 CST

Hi,
a quick question on the g(r) GUI plugin. I'm using it to calculate how
the presence of a small peptide perturbates
the water structure in its vicinity. I'm skipping the details of the
calculation here but I'm using the selection
"water and same residue as within XX from protein" with several values
of XX just to see how the perturbation decays.

Now, I'm reading on the VMD website:
 
"Note, that the normalization of g(r) has little meaning unless you
enable processing of the periodic boundary condition
and have a fixed set of atoms in the selection.
The number integrals are computed directly and thus provide accurate
coordination numbers."

Since I'm interested in the number integrals, I'd like to know if the
last line actually means that the number integrals are correct even if
the number of atoms varies from one frame to another

Thanks
Giovanni